A metabolic pathway for catabolizing levulinic acid in bacteria
Abstract
Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. Here, this discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.
- Authors:
-
[1]
- Univ. of Wisconsin, Madison, WI (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1399002
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Microbiology
- Additional Journal Information:
- Journal Volume: 2; Journal ID: ISSN 2058-5276
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES
Citation Formats
Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, and Pfleger, Brian F. A metabolic pathway for catabolizing levulinic acid in bacteria. United States: N. p., 2017.
Web. doi:10.1038/s41564-017-0028-z.
Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, & Pfleger, Brian F. A metabolic pathway for catabolizing levulinic acid in bacteria. United States. https://doi.org/10.1038/s41564-017-0028-z
Rand, Jacqueline M., Pisithkul, Tippapha, Clark, Ryan L., Thiede, Joshua M., Mehrer, Christopher R., Agnew, Daniel E., Campbell, Candace E., Markley, Andrew L., Price, Morgan N., Ray, Jayashree, Wetmore, Kelly M., Suh, Yumi, Arkin, Adam P., Deutschbauer, Adam M., Amador-Noguez, Daniel, and Pfleger, Brian F. Mon .
"A metabolic pathway for catabolizing levulinic acid in bacteria". United States. https://doi.org/10.1038/s41564-017-0028-z. https://www.osti.gov/servlets/purl/1399002.
@article{osti_1399002,
title = {A metabolic pathway for catabolizing levulinic acid in bacteria},
author = {Rand, Jacqueline M. and Pisithkul, Tippapha and Clark, Ryan L. and Thiede, Joshua M. and Mehrer, Christopher R. and Agnew, Daniel E. and Campbell, Candace E. and Markley, Andrew L. and Price, Morgan N. and Ray, Jayashree and Wetmore, Kelly M. and Suh, Yumi and Arkin, Adam P. and Deutschbauer, Adam M. and Amador-Noguez, Daniel and Pfleger, Brian F.},
abstractNote = {Microorganisms can catabolize a wide range of organic compounds and therefore have the potential to perform many industrially relevant bioconversions. One barrier to realizing the potential of biorefining strategies lies in our incomplete knowledge of metabolic pathways, including those that can be used to assimilate naturally abundant or easily generated feedstocks. For instance, levulinic acid (LA) is a carbon source that is readily obtainable as a dehydration product of lignocellulosic biomass and can serve as the sole carbon source for some bacteria. Yet, the genetics and structure of LA catabolism have remained unknown. Here, we report the identification and characterization of a seven-gene operon that enables LA catabolism in Pseudomonas putida KT2440. When the pathway was reconstituted with purified proteins, we observed the formation of four acyl-CoA intermediates, including a unique 4-phosphovaleryl-CoA and the previously observed 3-hydroxyvaleryl-CoA product. Using adaptive evolution, we obtained a mutant of Escherichia coli LS5218 with functional deletions of fadE and atoC that was capable of robust growth on LA when it expressed the five enzymes from the P. putida operon. Here, this discovery will enable more efficient use of biomass hydrolysates and metabolic engineering to develop bioconversions using LA as a feedstock.},
doi = {10.1038/s41564-017-0028-z},
journal = {Nature Microbiology},
number = ,
volume = 2,
place = {United States},
year = {2017},
month = {9}
}
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Works referenced in this record:
MicrobesOnline: an integrated portal for comparative and functional genomics
journal, November 2009
- Dehal, P. S.; Joachimiak, M. P.; Price, M. N.
- Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400
Compilation and analysis of 54-dependent promoter sequences
journal, November 1999
- Barrios, H.; Valderrama, B.; Morett, E.
- Nucleic Acids Research, Vol. 27, Issue 22
Function of MbtH homologs in nonribosomal peptide biosynthesis and applications in secondary metabolite discovery
journal, August 2011
- Baltz, Richard H.
- Journal of Industrial Microbiology & Biotechnology, Vol. 38, Issue 11
Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
journal, February 2013
- Qi, Lei S.; Larson, Matthew H.; Gilbert, Luke A.
- Cell, Vol. 152, Issue 5, p. 1173-1183
Bacterial production of short-chain organic acids and trehalose from levulinic acid: A potential cellulose-derived building block as a feedstock for microbial production
journal, February 2015
- Habe, Hiroshi; Sato, Shun; Morita, Tomotake
- Bioresource Technology, Vol. 177
High-titer production of monomeric hydroxyvalerates from levulinic acid in Pseudomonas putida
journal, January 2009
- Martin, Collin H.; Prather, Kristala L. Jones
- Journal of Biotechnology, Vol. 139, Issue 1
Regulation of the ato operon by the atoC gene in Escherichia coli.
journal, May 1987
- Jenkins, L. S.; Nunn, W. D.
- Journal of Bacteriology, Vol. 169, Issue 5
Levulinic Acid Biorefineries: New Challenges for Efficient Utilization of Biomass
journal, February 2016
- Pileidis, Filoklis D.; Titirici, Maria-Magdalena
- ChemSusChem, Vol. 9, Issue 6
Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes
journal, May 2009
- Striebel, Frank; Imkamp, Frank; Sutter, Markus
- Nature Structural & Molecular Biology, Vol. 16, Issue 6
Discovery and Characterization of a 5-Hydroxymethylfurfural Oxidase from Methylovorus sp. Strain MP688
journal, November 2013
- Dijkman, Willem P.; Fraaije, Marco W.
- Applied and Environmental Microbiology, Vol. 80, Issue 3
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome
journal, January 2009
- Díaz-Mejía, Juan Javier; Babu, Mohan; Emili, Andrew
- FEMS Microbiology Reviews, Vol. 33, Issue 1
The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: Evidence from proteomic and genomic analyses
journal, June 2009
- Moreno, Renata; Martínez-Gomariz, Montserrat; Yuste, Luis
- PROTEOMICS, Vol. 9, Issue 11, p. 2910-2928
Integrated Bioprocessing for the pH-Dependent Production of 4-Valerolactone from Levulinate in Pseudomonas putida KT2440
journal, November 2009
- Martin, C. H.; Wu, D.; Prather, K. L. J.
- Applied and Environmental Microbiology, Vol. 76, Issue 2
Biopython: freely available Python tools for computational molecular biology and bioinformatics
journal, March 2009
- Cock, P. J. A.; Antao, T.; Chang, J. T.
- Bioinformatics, Vol. 25, Issue 11
Mesoporous H3PW12O40-silica composite: Efficient and reusable solid acid catalyst for the synthesis of diphenolic acid from levulinic acid
journal, June 2008
- Guo, Yihang; Li, Kexin; Yu, Xiaodan
- Applied Catalysis B: Environmental, Vol. 81, Issue 3-4
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons
journal, May 2015
- Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.
- mBio, Vol. 6, Issue 3, Article No. e00306-15
Oxidation of propionate to pyruvate in Escherichia coli: Involvement of methylcitrate dehydratase and aconitase
journal, December 2002
- Brock, Matthias; Maerker, Claudia; Schütz, Alexandra
- European Journal of Biochemistry, Vol. 269, Issue 24
Gamma-valerolactone, a sustainable platform molecule derived from lignocellulosic biomass
journal, January 2013
- Alonso, David Martin; Wettstein, Stephanie G.; Dumesic, James A.
- Green Chemistry, Vol. 15, Issue 3
Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009
- Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
- Nature Methods, Vol. 6, Issue 5, p. 343-345
Catabolism of 4-Hydroxyacids and 4-Hydroxynonenal via 4-Hydroxy-4-phosphoacyl-CoAs
journal, September 2009
- Zhang, Guo-Fang; Kombu, Rajan S.; Kasumov, Takhar
- Journal of Biological Chemistry, Vol. 284, Issue 48
Development of a Method for Markerless Gene Deletion in Pseudomonas putida
journal, June 2011
- Graf, Nadja; Altenbuchner, Josef
- Applied and Environmental Microbiology, Vol. 77, Issue 15
Efficient Conversion of Furfuryl Alcohol into Alkyl Levulinates Catalyzed by an Organic-Inorganic Hybrid Solid Acid Catalyst
journal, January 2011
- Zhang, Zehui; Dong, Kun; Zhao, Zongbao Kent
- ChemSusChem, Vol. 4, Issue 1
Synthesis and Applications of Alkyl Levulinates
journal, May 2014
- Démolis, Alexandre; Essayem, Nadine; Rataboul, Franck
- ACS Sustainable Chemistry & Engineering, Vol. 2, Issue 6
FliT Acts as an Anti-FlhD2C2 Factor in the Transcriptional Control of the Flagellar Regulon in Salmonella enterica Serovar Typhimurium
journal, September 2006
- Yamamoto, S.; Kutsukake, K.
- Journal of Bacteriology, Vol. 188, Issue 18
Interactions of the Antizyme AtoC with Regulatory Elements of the Escherichia coli atoDAEB Operon
journal, July 2007
- Matta, M. K.; Lioliou, E. E.; Panagiotidis, C. H.
- Journal of Bacteriology, Vol. 189, Issue 17
Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System
journal, January 2015
- Jiang, Yu; Chen, Biao; Duan, Chunlan
- Applied and Environmental Microbiology, Vol. 81, Issue 7, p. 2506-2514
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
journal, November 2013
- Espah Borujeni, Amin; Channarasappa, Anirudh S.; Salis, Howard M.
- Nucleic Acids Research, Vol. 42, Issue 4
Global Topology Analysis of the Escherichia coli Inner Membrane Proteome
journal, May 2005
- Daley, D. O.
- Science, Vol. 308, Issue 5726
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing
journal, September 2015
- Li, Yifan; Lin, Zhenquan; Huang, Can
- Metabolic Engineering, Vol. 31, p. 13-21
Small Proteins Can No Longer Be Ignored
journal, June 2014
- Storz, Gisela; Wolf, Yuri I.; Ramamurthi, Kumaran S.
- Annual Review of Biochemistry, Vol. 83, Issue 1
Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
journal, June 2011
- Goto, Hiroki; Dickins, Benjamin; Afgan, Enis
- Genome Biology, Vol. 12, Issue 6
A simple and reliable 5'-RACE approach
journal, November 2000
- Schramm, G.
- Nucleic Acids Research, Vol. 28, Issue 22
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria
journal, January 2009
- Pinto, Fernando; Thapper, Anders; Sontheim, Wolfgang
- BMC Molecular Biology, Vol. 10, Issue 1
Homo- and Co-Polycarbonates and Blends Derived from Diphenolic Acid
journal, June 2001
- Moore, J. A.; Tannahill, T.
- High Performance Polymers, Vol. 13, Issue 2
The Enigmatic Escherichia coli fadE Gene Is yafH
journal, July 2002
- Campbell, J. W.; Cronan, J. E.
- Journal of Bacteriology, Vol. 184, Issue 13
pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes
journal, January 2011
- Martínez-García, Esteban; Calles, Belén; Arévalo-Rodríguez, Miguel
- BMC Microbiology, Vol. 11, Issue 1
Basic local alignment search tool
journal, October 1990
- Altschul, Stephen F.; Gish, Warren; Miller, Webb
- Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
Maltodextrin-binding proteins from diverse bacteria and archaea are potent solubility enhancers
journal, January 2003
- Fox, Jeffrey D.; Routzahn, Karen M.; Bucher, Matthew H.
- FEBS Letters, Vol. 537, Issue 1-3
The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation
journal, October 2009
- Moreno, R.; Marzi, S.; Romby, P.
- Nucleic Acids Research, Vol. 37, Issue 22
Studies on the nonmevalonate pathway to terpenes: The role of the GcpE (IspG) protein
journal, December 2001
- Hecht, S.; Eisenreich, W.; Adam, P.
- Proceedings of the National Academy of Sciences, Vol. 98, Issue 26
Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system.
journal, January 1987
- Jenkins, L. S.; Nunn, W. D.
- Journal of Bacteriology, Vol. 169, Issue 1
Enzymatic reduction of levulinic acid by engineering the substrate specificity of 3-hydroxybutyrate dehydrogenase
journal, April 2013
- Yeon, Young Joo; Park, Hyung-Yeon; Yoo, Young Je
- Bioresource Technology, Vol. 134
The initial metabolic conversion of levulinic acid in Cupriavidus necator
journal, September 2011
- Jaremko, Matt; Yu, Jian
- Journal of Biotechnology, Vol. 155, Issue 3
Production of levulinic acid and use as a platform chemical for derived products
journal, February 2000
- Bozell, Joseph J.; Moens, L.; Elliott, D. C.
- Resources, Conservation and Recycling, Vol. 28, Issue 3-4, p. 227-239
The binding of propionyl-CoA and carboxymethyl-CoA to Escherichia coli citrate synthase
journal, July 1995
- Man, Wai-Jin; Li, Yan; David O'Connor, C.
- Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1250, Issue 1, p. 69-75
MbtH-Like Proteins as Integral Components of Bacterial Nonribosomal Peptide Synthetases
journal, October 2010
- Felnagle, Elizabeth A.; Barkei, John J.; Park, Hyunjun
- Biochemistry, Vol. 49, Issue 41
Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum
journal, July 1994
- Schäfer, Andreas; Tauch, Andreas; Jäger, Wolfgang
- Gene, Vol. 145, Issue 1, p. 69-73
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013
- Jiang, Wenyan; Bikard, David; Cox, David
- Nature Biotechnology, Vol. 31, Issue 3, p. 233-239
Metabolism of Levulinate in Perfused Rat Livers and Live Rats: CONVERSION TO THE DRUG OF ABUSE 4-HYDROXYPENTANOATE
journal, December 2010
- Harris, Stephanie R.; Zhang, Guo-Fang; Sadhukhan, Sushabhan
- Journal of Biological Chemistry, Vol. 286, Issue 7
Ethyl levulinate: A potential bio-based diluent for biodiesel which improves cold flow properties
journal, July 2011
- Joshi, Hem; Moser, Bryan R.; Toler, Joe
- Biomass and Bioenergy, Vol. 35, Issue 7
Culture Medium for Enterobacteria
journal, January 1974
- Neidhardt, Frederick C.; Bloch, Philip L.; Smith, David F.
- Journal of Bacteriology, Vol. 119, Issue 3
Works referencing / citing this record:
Genetic tools for reliable gene expression and recombineering in Pseudomonas putida
journal, January 2018
- Cook, Taylor B.; Rand, Jacqueline M.; Nurani, Wasti
- Journal of Industrial Microbiology & Biotechnology, Vol. 45, Issue 7
The Use of Azohydromonas lata DSM 1122 to Produce 4-hydroxyvalerate-Containing Polyhydroxyalkanoate Terpolymers, and Unique Polymer Blends from Mixed-Cultures with Burkholderia sacchari DSM 17165
journal, November 2018
- Ashby, Richard D.; Solaiman, Daniel K. Y.; Strahan, Gary D.
- Journal of Polymers and the Environment, Vol. 27, Issue 1
High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities
journal, November 2019
- Nogales, Juan; Mueller, Joshua; Gudmundsson, Steinn
- Environmental Microbiology, Vol. 22, Issue 1
Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
journal, July 2018
- Zhalnina, Kateryna; Zengler, Karsten; Newman, Dianne
- mBio, Vol. 9, Issue 4
Draft Genome Sequence of Pseudomonas citronellolis LA18T, a Bacterium That Uses Levulinic Acid
journal, August 2018
- Inaba, Tomohiro; Sato, Yuya; Koike, Hideaki
- Microbiology Resource Announcements, Vol. 7, Issue 5
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism
journal, February 2019
- Price, Morgan N.; Ray, Jayashree; Iavarone, Anthony T.
- mSystems, Vol. 4, Issue 1
Identification and characterization of levulinyl-CoA synthetase from Pseudomonas citronellolis, which differs phylogenetically from LvaE of Pseudomonas putida
journal, August 2019
- Habe, Hiroshi; Koike, Hideaki; Sato, Yuya
- AMB Express, Vol. 9, Issue 1